Objectives: Cryptosporidium, a protozoan parasite, has been recognized as a frequent cause of waterborne disease due to its extremely strong resistance against chlorine disinfection. Although there has as yet been no report of a Cryptosporidium outbreak through drinking water in Korea, it is important to estimate the health risk of Cryptosporidium in water supply systems because of the various infection cases in human and domestic animals and frequent detection reports on their oocysts in water environments. Methods: This study evaluated the annual infection risk of Cryptosporidium in tap water using the quantitative microbial risk assessment technique. Exposure assessment was performed upon the results of a national survey on Cryptosporidium on the water sources of 97 large-scale water purification plants in Korea, water treatment efficacy, and daily unboiled tap water consumption. The estimates of the US Environmental Protection Agency on the mean likelihood of infection from ingesting one oocyst were applied for effect assessment. Results: Using probabilistic methods, mean annual infection risk of Cryptosporidiosis by the intake of tap water was estimated to fall within the range of $2.3{ imes}10^{-4}$ to $1.0{ imes}10^{-3}$ (median $5.7{ imes}10^{-4}$). The risk in using river sources was predicted to be four times higher than with lake sources. With 0.5-log higher removal efficacy, the risk was estimated to be $1.8{ imes}10^{-4}$, and could then be lowered by one-third. Conclusions: These estimations can be compared with acceptable risk and then used to determine the adequacy and priority of various drinking water quality strategies such as the establishment of new treatment technology.